Yep, had the very same problem with a 2000A keyboard (square LED on the front of the caps lock key) hooked up to my 500. The only way to get around it was to switch back to the original keyboard (the adapter I built had a switch from the start).
Should really work the same way with a 500 kb on a 2000 - I guess you mixed up clock & data. Actually, all Amiga keyboards work the same. The only difference is the reset signal which is encoded with a long clock low on some and a separate line on others.
I've been told that you can actually attach more than a single keyboard at once w/o switching, but I've never tried that.
